4P2C

Complex of Shiga toxin 2e with a neutralizing single-domain antibody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4p2ca_	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	Shiga toxin, A-chain	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d4p2cc_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d4p2cd_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d4p2cf_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d4p2cb_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d4p2ce_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d4p2cg_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
H	d4p2ch_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
I	d4p2ci_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
J	d4p2cj1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
J	d4p2cj2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
K	d4p2ck_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Shiga toxin A-chain	8073995	4002413	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribosome inactivating proteins (RIP)	8073996	3001164	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Bacterial enterotoxins	8099446	3000434	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bacterial enterotoxins	8099446	3000434	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Bacterial enterotoxins	8099446	3000434	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacterial enterotoxins	8099446	3000434	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Bacterial enterotoxins	8099446	3000434	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00161	e4p2cA1	A: a+b two layers	X: RIP/Polo-box domain	H: Ribosome inactivating proteins (RIP) (From Topology)	T: Ribosome inactivating proteins (RIP)	F: PF00161	ECOD (1.6)
C	PF02258	e4p2cC1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: PF02258	ECOD (1.6)
D	PF02258	e4p2cD1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: PF02258	ECOD (1.6)
F	PF02258	e4p2cF1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: PF02258	ECOD (1.6)
B	PF02258	e4p2cB1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: PF02258	ECOD (1.6)
E	PF02258	e4p2cE1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: PF02258	ECOD (1.6)
G	PF07686	e4p2cG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H	PF07686	e4p2cH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I	PF07686	e4p2cI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
J	PF07686	e4p2cJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
K	PF07686	e4p2cK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.420.10	Alpha Beta	3-Layer(aba) Sandwich	Ricin (A subunit)	domain 1	CATH (4.3.0)
A	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (4.3.0)
C	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
F	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
E	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
G, H, I, J, K	Nanobody 1, Anti-F4+ETEC bacteria	VH	Lama glama (llama)	IGHV3S301, IGHJ401	V-DOMAIN VH	IG	(VH)	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G, H, I, J, K	Heavy Chain	IGHV1	-	shiga toxin 2e, subunit b \| shiga toxin 2e, subunit a, shiga toxin 2e, subunit b	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00161	Ribosome inactivating protein (RIP)	Ribosome inactivating protein	-	Domain
B, C, D, E, F	PF02258	Shiga-like toxin beta subunit (SLT_beta)	Shiga-like toxin beta subunit	This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of E.coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT's are composed of one enzymatic A subunit and five cell binding B s ...	This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of E.coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT's are composed of one enzymatic A subunit and five cell binding B subunits.	Domain
G, H, I, J, K	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Shiga toxin 2e, subunit A	hydrolase activity, acting on glycosyl bonds rRNA N-glycosylase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity, acting on a rRNA catalytic activity RNA glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds toxin activity	regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process	-
B, C, D, E, F	Shiga toxin 2e, subunit B	-	biological process involved in interspecies interaction between organisms symbiont-mediated cytolysis of host cell disruption of cell in another organism hemolysis by symbiont of host erythrocytes cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction cytolysis in another organism cellular process disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing	extracellular region cellular anatomical entity
G, H, I, J, K	Nanobody 1, Anti-F4+ETEC bacteria VHH variable region	-	response to stimulus immune response immune system process adaptive immune response	protein-containing complex immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
A	IPR016331	Shiga-like toxin, subunit A	Family
A	IPR017988	Ribosome-inactivating protein conserved site	Conserved Site
A	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
A	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
A	IPR001574	Ribosome-inactivating protein	Family
B, C, D, E, F	IPR008992	Enterotoxin	Homologous Superfamily
B, C, D, E, F	IPR003189	Shiga-like toxin, beta subunit	Family
G, H, I, J, K	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
G, H, I, J, K	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
G, H, I, J, K	IPR003599	Immunoglobulin subtype	Domain
G, H, I, J, K	IPR013106	Immunoglobulin V-set domain	Domain
G, H, I, J, K	IPR007110	Immunoglobulin-like domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.